I don't remember much of the older games, but I had one difficult/annoying level just a few days ago while playing Catherine on the xbox360. Stage 5 of the nightmare on hardest difficultly.
I'm amazed my controller didn't break.

I remember mega man not to be faceroll, my progress were much slower than in any other nintendo games I played back in those days. Dont remember if it was first megaman or second, but I remember it being hard. I dont know how old I was back then, which year did nes have its primetime? I cant have been that many years and that could have been a reason why I considered it difficult =)

As a bigtime Battletoads player I need to break it to you and say that Turbo Tunnel is one of the easier stages in the game. That by no means makes it easy, it's still very hard by normal game standards, but there are stages heaps harder than that in the game. Terra Tubes is harder for example, the sharks and fishes are always a kick in the nuts. Volkmire's Inferno is easily a much harder version of Turbo Tunnel. Karnath's Lair (Snake stage) is also a lot harder because of the 4th room. Intruder Excluder is a tad harder too, not by much though. The Revolution is also harder, but maybe that's because you don't get to practice that as much since its the last stage. Clinger Winger, oh fucking hell no, that's quite near impossible.

However, if we're talking the most frustrating stage, Rat Race takes it. It makes me so stressed it goes beyond being pissed and puts me in a depressive mood for the rest of the day. That's the true turd of Battletoads, while Turbo Tunnel is where most people get stuck, if they ever pass it they'll learn that the game only gets harder from there on. Rat Race is the peak, not necessarily because its the hardest stage, but it is by far the most stressing, one bad turn can cost you the stage. Fuck that stage.

Oh, and you missed Stage 6 in Ninja Gaiden, that stage is also renowned for being shitly hard, and its at least a lot harder than The Great Maze on Intense, which I didn't find all that hard tbh. What am I saying? Its your list, I shouldn't try and control it. Still, I think that it needed mention in here.

I know we're all going retro, but I have to put forward Super Meat Boy. Makes the toughest Nintendo vets cry.

Super Meat Boy is a great game, but it doesn't make "the toughest Nintendo vets" cry, sure its up to par with the old broken games, but not up to par with Silver Surfer or Battletoads. The people who made Super Meat Boy knew what they were doing, with old games people didn't know how to tune the difficulty properly, making it become nearly impossible. Still, it definitely deserves a mention.

Water Temple? Seriously? Naaaw. Only annoying thing about it was the need to revisit rooms because of changing water levels and the scenery was pretty dull and boring. Places like the Fire Temple offered more to look at and in terms of variation.

Plus the Water Temple holds one of my favorite encounters: The fight against Shadow Link. I just loved that part, although Nintendo could've made so much more out of this encounter and the general idea of a dark and twisted shadow persona.

i'd have to disagree with all the N64 selections. None of those games took me more than a couple sittings to play through (I was in middle school when the system first dropped). IMO the dark maze in Zelda II was the hardest level I ever played in a game. Hell that whole game was fairly frustrating, especially when it would randomly decide to erase my saved game 80% of the way through.